Statistical Mechanics of Biological Sequence Analysis

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This award supports theoretical research and education at the interface between condensed matter physics and biology. The biological sciences are undergoing a revolutionary change fueled in part by the emergence of experimental techniques that produce massive amounts of quantitative biological data that need to be transformed into understanding of biological systems. The PI will use statistical physics tools to develop new methods to predict the location of new genes and of RNA editing sites in the mitochondrial genome of the slime mold Physarum polycephalum. This organism edits its messenger RNAs so that the translated messenger RNA sequence of a gene differs from its genomic sequence. This RNA editing leads to a failure of conventional gene prediction techniques. New transfer matrix algorithms aware of RNA editing will identify genes, pinpoint editing sites, and shed light on the functioning of the editing machinery. This project can be described in terms of a physical system with a complex energy landscape. Beyond applying physical ideas to biological systems, this interdisciplinary research also advances condensed matter physics by opening new frontiers of inquiry and by advancing the statistical physics of disordered systems.This award supports education at the undergraduate and graduate levels. Students will learn computational techniques and concepts from condensed matter physics and molecular biology. This helps provide well-trained individuals for the modern workforce with a background that is at once strong in biology and quantitative physical science. Through the development of undergraduate and graduate courses in biophysics the base of students with an interdisciplinary education will be expanded beyond the individuals immediately involved in the research projects. The project will also yield new algorithms for the interpretation of quantitative biological data. Algorithms developed in the course of the research will be accessible to the broader materials research and scientific communities. %%%This award supports theoretical research and education at the interface between condensed matter physics and biology. The biological sciences are undergoing a revolutionary change fueled in part by the emergence of experimental techniques that produce massive amounts of quantitative biological data that need to be transformed into understanding of biological systems. This research focuses on RNA-editing which occurs in organisms as diverse as the Ebola virus and humans. Most genes are copied into messenger RNA sequences that are in turn translated into proteins. In organisms exhibiting RNA-editing, special machinery operates to modify the messenger RNA before it is translated into proteins. This complicates the identification of genes that result in the creation of specific proteins. It also raises interesting questions about how the process works and why it is so reliable. The PI will use statistical physics tools to develop new methods to predict the location of new genes and of RNA editing sites in the mitochondrial genome of the slime mold Physarum polycephalum. Beyond applying physical ideas to biological systems, this interdisciplinary research also advances condensed matter physics by opening new frontiers of inquiry and by advancing the statistical physics of disordered systems.This award supports education at the undergraduate and graduate levels. Students will learn computational techniques and concepts from condensed matter physics and molecular biology. This helps provide well-trained individuals for the modern workforce with a background that is at once strong in biology and quantitative physical science. Through the development of undergraduate and graduate courses in biophysics the base of students with an interdisciplinary education will be expanded beyond the individuals immediately involved in the research projects. The project will also yield new algorithms for the interpretation of quantitative biological data. Algorithms developed in the course of the research will be accessible to the broader materials research and scientific communities.***